In the spring of 1776 he and his troops (including his young son Jonathan) were sent to support an invasion of Canada, but were diverted to New York's Mohawk Valley where Colonel Dayton was put in charge of constructing fortifications to protect the colonists from Loyalist and Indian insurrections. These fortifications included Fort Dayton in what is now Herkimer, New York.

In December 1778, New Jersey named him as a delegate to the Continental Congress, but he remained with the army and did not attend the Congress. He was promoted to brigadier general in the Continental Army in 1783, and later to major general of militia.